Hi all, I was having trouble to install the rsbml package and it complains about not having the ParseMessage.h file in the libsbml include directory. Does rsbml actually requires version 3 of libsbml? Any one has a clue? Thanks a lot! best, jie * installing *source* package ?rsbml? ... checking for pkg-config... /opt/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for LIBSBML3... no checking for gcc... /opt/local/bin/gcc-mp-4.4 -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /opt/local/bin/gcc-mp-4.4 -std=gnu99 accepts -g... yes checking for /opt/local/bin/gcc-mp-4.4 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... /opt/local/bin/gcc-mp-4.4 -std=gnu99 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking sbml/xml/ParseMessage.h usability... no checking sbml/xml/ParseMessage.h presence... no checking for sbml/xml/ParseMessage.h... no configure: error: Could not find sbml/xml/ParseMessage.h: rsbml requires libsbml from http://www.sbml.org/software/libsbml/ use --with-libsbml-include or LIBSBML_INCLUDE to specify the include path. ERROR: configuration failed for package ?rsbml? * removing ?/Users/bao/R/i386-apple-darwin9.8.0-library/2.13/rsbml? The downloaded packages are in ?/private/var/folders/Up/UpTpxqkaGMmzlCOlJBc+pk+++TI/-Tmp-/Rtm p6enfxM/downloaded_packages? Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'rsbml' had non-zero exit status > sessionInfo() R version 2.13.0 (2011-04-13) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.0 -- Freiburg Institute for Advanced Studies - FRIAS School of Life Sciences - LIFENET Albert-Ludwigs-Universit?t Freiburg Albertstr. 19 79104 Freiburg Germany T.: +49-761-203-97207

On Wed, Jun 22, 2011 at 3:28 AM, Jie Bao <jie.bao@frias.uni- freiburg.de="">wrote: > Hi all, > > I was having trouble to install the rsbml package and it complains > about not having the ParseMessage.h file in the libsbml include > directory. Does rsbml actually requires version 3 of libsbml? Any one > has a clue? Thanks a lot! > > Which version of libsbml do you have? I would recommend using 3.x as 2.x is getting pretty long in the tooth (5.x is current). But rsbml will still work with 2.x; you just have to tell it where to look, as described by the error message. Michael > best, > jie > > > * installing *source* package ‘rsbml’ ... > checking for pkg-config... /opt/local/bin/pkg-config > checking pkg-config is at least version 0.9.0... yes > checking for LIBSBML3... no > checking for gcc... /opt/local/bin/gcc-mp-4.4 -std=gnu99 > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether /opt/local/bin/gcc-mp-4.4 -std=gnu99 accepts -g... yes > checking for /opt/local/bin/gcc-mp-4.4 -std=gnu99 option to accept ISO > C89... none needed > checking how to run the C preprocessor... /opt/local/bin/gcc-mp-4.4 > -std=gnu99 -E > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking sbml/xml/ParseMessage.h usability... no > checking sbml/xml/ParseMessage.h presence... no > checking for sbml/xml/ParseMessage.h... no > configure: error: Could not find sbml/xml/ParseMessage.h: > rsbml requires libsbml from http://www.sbml.org/software/libsbml/ > use --with-libsbml-include or LIBSBML_INCLUDE to specify the include > path. > ERROR: configuration failed for package ‘rsbml’ > * removing ‘/Users/bao/R/i386-apple-darwin9.8.0-library/2.13/rsbml’ > > The downloaded packages are in > > ‘/private/var/folders/Up/UpTpxqkaGMmzlCOlJBc+pk+++TI/-Tmp-/Rtmp6enf xM/downloaded_packages’ > Warning message: > In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'rsbml' had non-zero exit status > > sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.13.0 > > -- > Freiburg Institute for Advanced Studies - FRIAS > School of Life Sciences - LIFENET > Albert-Ludwigs-Universität Freiburg > Albertstr. 19 > 79104 Freiburg > Germany > T.: +49-761-203-97207 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]